Is it possible to save pose to model
If you want to apply the shape of the object as deformed by the armature, what you can do is select the object being deformed, and go to the modifiers tab.
In the modifiers tab, you will see a modifier "Armature deform". Apply this modifier not as a shape key if you want to permanently keep the shape, and as a shape key if you want to toggle between the original shape, and it's deformed shape. From what I saw in your question, this should solve your problem.